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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ), 'gf_id' => 'HOM05D001163', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001163' ), 'data_identifier' => 'HOM05D001163', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001163', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '531', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11910' => 'bna', 'A01p41720' => 'bna', 'A04p26650' => 'bna', 'A05p10760' => 'bna', 'A05p38670' => 'bna', 'A07p18460' => 'bna', 'A08p10930' => 'bna', 'A09p35290' => 'bna', 'A10p31630' => 'bna', 'Aa31LG11G5320' => 'aar', 'Aa31LG3G3360' => 'aar', 'Aa31LG5G8130' => 'aar', 'Aa31LG6G12280' => 'aar', 'Aa31LG6G2590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1496' => 'aag', 'Actinidia06719' => 'ach', 'Actinidia07192' => 'ach', 'Actinidia18556' => 'ach', 'Actinidia34787' => 'ach', 'Actinidia38893' => 'ach', 'Ah.04g163560' => 'amhyb', 'Ah.08g212290' => 'amhyb', 'AL1G45150' => 'aly', 'AL4G22270' => 'aly', 'AL4G30930' => 'aly', 'AL6G14090' => 'aly', 'AL8G14850' => 'aly', 'Aqoxy1G01048' => 'aox', 'Aqoxy1G01366' => 'aox', 'arahy.Tifrunner.gnm1.ann1.60YUP7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.63SYA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7K6UQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EIQP1Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZDG1A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IEY1AM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3U4LA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3VXN8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PN4BM4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PY5VJM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHM2EA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WK0KEV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X1BST6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X5K9YD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XP2BFV' => 'arhy', 'AT1G30860' => 'ath', 'AT2G27950' => 'ath', 'AT2G34920' => 'ath', 'AT4G20160' => 'ath', 'AT5G04460' => 'ath', 'AT5G44690' => 'ath', 'ATR0043G042' => 'atr', 'ATR0794G092' => 'atr', 'Atru.chr10.243' => 'acertr', 'Atru.chr12.912' => 'acertr', 'Atru.chr12.913' => 'acertr', 'Atru.chr12.914' => 'acertr', 'Atru.chr3.3497' => 'acertr', 'AUR62024031' => 'cqu', 'AUR62041258' => 'cqu', 'AUR62041313' => 'cqu', 'AUR62043092' => 'cqu', 'BcaB02g09496' => 'bca', 'BcaB02g09497' => 'bca', 'BcaB02g09498' => 'bca', 'BcaB02g10125' => 'bca', 'BcaB03g16567' => 'bca', 'BcaB04g18202' => 'bca', 'BcaB06g28820' => 'bca', 'BcaB06g28823' => 'bca', 'BcaB07g30503' => 'bca', 'BcaB07g32752' => 'bca', 'BcaC02g07748' => 'bca', 'BcaC02g10918' => 'bca', 'BcaC02g11575' => 'bca', 'BcaC03g16688' => 'bca', 'BcaC05g27124' => 'bca', 'BcaC05g29456' => 'bca', 'BcaC06g32153' => 'bca', 'BcaC06g32154' => 'bca', 'BcaC06g32155' => 'bca', 'BcaC07g37799' => 'bca', 'BcaC09g51332' => 'bca', 'BcaNung03710' => 'bca', 'BcaNung04929' => 'bca', 'BcaNung07202' => 'bca', 'BolC1t01379H' => 'bol', 'BolC1t05390H' => 'bol', 'BolC2t10557H' => 'bol', 'BolC4t22975H' => 'bol', 'BolC4t23866H' => 'bol', 'BolC4t27883H' => 'bol', 'BolC5t31745H' => 'bol', 'BolC5t34411H' => 'bol', 'BolC8t48190H' => 'bol', 'BolC9t59974H' => 'bol', 'BraA01t01133Z' => 'bra', 'BraA01t04247Z' => 'bra', 'BraA04t18170Z' => 'bra', 'BraA05t20020Z' => 'bra', 'BraA05t22658Z' => 'bra', 'BraA07t29562Z' => 'bra', 'BraA08t33090Z' => 'bra', 'BraA09t39058Z' => 'bra', 'BraA10t45209Z' => 'bra', 'C01p14150' => 'bna', 'C04p13870' => 'bna', 'C04p23690' => 'bna', 'C04p64070' => 'bna', 'C05p30090' => 'bna', 'C05p57540' => 'bna', 'C09p72300' => 'bna', 'CAN.G370.76' => 'can', 'CANSAT35G1654' => 'cansat', 'CANSAT56G0151' => 'cansat', 'CANSAT64G0711' => 'cansat', 'CARHR030350' => 'chi', 'CARHR085020' => 'chi', 'CARHR120660' => 'chi', 'CARHR129070' => 'chi', 'CARHR208810' => 'chi', 'CARHR226990' => 'chi', 'Carub.0001s2920' => 'cru', 'Carub.0004s0871' => 'cru', 'Carub.0004s1660' => 'cru', 'Carub.0006s0339' => 'cru', 'Carub.0007s2097' => 'cru', 'Carub.0008s0357' => 'cru', 'Ca_01701_v3' => 'car', 'Ca_02402_v3' => 'car', 'Ca_10456_v3' => 'car', 'Ca_10760_v3' => 'car', 'Ca_18216_v3' => 'car', 'CBR_g19901' => 'cbr', 'Cc01_g10160' => 'ccan', 'Cc02_g10550' => 'ccan', 'Cc09_g04670' => 'ccan', 'CDE02G1544' => 'cde', 'CDE03G0138' => 'cde', 'CDE05G3208' => 'cde', 'CDE06G0768' => 'cde', 'CDE06G1402' => 'cde', 'CDE08G1589' => 'cde', 'Cfa001158' => 'cfa', 'Cfa001773' => 'cfa', 'Cfa010135' => 'cfa', 'Ciclev10014128m.g' => 'ccl', 'Ciclev10027818m.g' => 'ccl', 'Ciclev10030689m.g' => 'ccl', 'CiPaw.01G265000' => 'cil', 'CiPaw.02G169900' => 'cil', 'CiPaw.09G140200' => 'cil', 'CiPaw.13G144500' => 'cil', 'CiPaw.14G106300' => 'cil', 'ClCG01G025930' => 'cla', 'ClCG05G021440' => 'cla', 'ClCG10G008440' => 'cla', 'COL.COLO4_19220' => 'col', 'COL.COLO4_25029' => 'col', 'COL.COLO4_32880' => 'col', 'Cpa.g.c27631.2' => 'cpa', 'Cpa.g.sc47.12' => 'cpa', 'Cpa.g.sc53.170' => 'cpa', 'CsaV3_5G035810' => 'csa', 'CsaV3_6G014460' => 'csa', 'CsaV3_6G053140' => 'csa', 'CSS0007886' => 'camsi', 'CSS0012349' => 'camsi', 'CSS0029005' => 'camsi', 'CSS0030005' => 'camsi', 'CSS0030119' => 'camsi', 'CSS0033081' => 'camsi', 'CSS0038695' => 'camsi', 'CSS0042627' => 'camsi', 'CSS0042764' => 'camsi', 'CSS0048305' => 'camsi', 'DCAR_004358' => 'dca', 'DCAR_006388' => 'dca', 'DCAR_015499' => 'dca', 'DCAR_018756' => 'dca', 'Dinv12572' => 'din', 'Dinv16242' => 'din', 'Dinv17882' => 'din', 'Dinv18039' => 'din', 'Dinv18040' => 'din', 'Dinv29389' => 'din', 'Dinv31266' => 'din', 'Dinv36358' => 'din', 'Duzib106G1239' => 'dzi', 'Duzib114G0656' => 'dzi', 'Duzib128G0028' => 'dzi', 'Duzib132G0266' => 'dzi', 'Duzib168G2055' => 'dzi', 'ECA232G1323' => 'eca', 'ECA233G3636' => 'eca', 'ECA233G4552' => 'eca', 'ECA238G2182' => 'eca', 'ECA238G3617' => 'eca', 'ECA248G0879' => 'eca', 'EL10Ac2g03347' => 'bvu', 'EL10Ac2g04763' => 'bvu', 'EL10Ac3g07317' => 'bvu', 'EL10Ac4g08629' => 'bvu', 'EL10Ac4g08632' => 'bvu', 'EL10Ac9g21003' => 'bvu', 'Eucgr.E04326' => 'egr', 'Eucgr.G02736' => 'egr', 'Eucgr.J00394' => 'egr', 'FAN01G1559' => 'fan', 'FAN03G3273' => 'fan', 'FAN06G1746' => 'fan', 'FAN10G3476' => 'fan', 'FAN11G0081' => 'fan', 'FAN11G3010' => 'fan', 'FAN16G0054' => 'fan', 'FAN16G2557' => 'fan', 'FAN21G1127' => 'fan', 'FAN21G1489' => 'fan', 'FAN25G2281' => 'fan', 'FAN25G3497' => 'fan', 'FvH4_3g13290' => 'fve', 'FvH4_3g30470' => 'fve', 'FvH4_7g06660' => 'fve', 'Glyma.09G048200' => 'gma', 'Glyma.10G198600' => 'gma', 'Glyma.11G191900' => 'gma', 'Glyma.12G082400' => 'gma', 'Glyma.12G179300' => 'gma', 'Glyma.13G321300' => 'gma', 'Glyma.15G155500' => 'gma', 'Glyma.16G119100' => 'gma', 'Glyma.20G191400' => 'gma', 'Gohir.A01G129400' => 'ghi', 'Gohir.A03G218400' => 'ghi', 'Gohir.A05G084700' => 'ghi', 'Gohir.A05G291020' => 'ghi', 'Gohir.A07G105500' => 'ghi', 'Gohir.A09G087700' => 'ghi', 'Gohir.A10G200200' => 'ghi', 'Gohir.A12G050800' => 'ghi', 'Gohir.D01G118200' => 'ghi', 'Gohir.D02G240300' => 'ghi', 'Gohir.D05G087500' => 'ghi', 'Gohir.D05G292150' => 'ghi', 'Gohir.D05G292201' => 'ghi', 'Gohir.D07G109500' => 'ghi', 'Gohir.D09G087600' => 'ghi', 'Gohir.D10G208100' => 'ghi', 'Gohir.D12G049100' => 'ghi', 'Gorai.001G117600' => 'gra', 'Gorai.002G143900' => 'gra', 'Gorai.005G268800' => 'gra', 'Gorai.006G104000' => 'gra', 'Gorai.008G052000' => 'gra', 'Gorai.009G089300' => 'gra', 'Gorai.009G308200' => 'gra', 'Gorai.011G233800' => 'gra', 'GSVIVG01010075001' => 'vvi', 'GSVIVG01016162001' => 'vvi', 'GSVIVG01031449001' => 'vvi', 'HanXRQChr01g0019481' => 'han', 'HanXRQChr05g0138031' => 'han', 'HanXRQChr05g0151581' => 'han', 'HanXRQChr08g0218291' => 'han', 'HanXRQChr09g0257871' => 'han', 'HanXRQChr11g0335981' => 'han', 'HanXRQChr13g0403581' => 'han', 'HanXRQChr14g0438941' => 'han', 'HanXRQChr14g0439011' => 'han', 'HanXRQChr14g0456141' => 'han', 'HanXRQChr16g0519871' => 'han', 'HanXRQChr16g0520861' => 'han', 'Haze_05193' => 'cav', 'Haze_16778' => 'cav', 'Haze_23521' => 'cav', 'Hma1.2p1_0051F.1_g029600' => 'hma', 'Hma1.2p1_0082F.1_g042580' => 'hma', 'Hma1.2p1_0454F.1_g156250' => 'hma', 'HPP92_014195' => 'vpl', 'HPP92_017572' => 'vpl', 'HPP92_022575' => 'vpl', 'HPP92_025775' => 'vpl', 'HPP92_026451' => 'vpl', 'HPP92_028319' => 'vpl', 'HPP92_028325' => 'vpl', 'Hund00846' => 'sun', 'Hund06765' => 'sun', 'Hund07753' => 'sun', 'Lalb_Chr02g0151121' => 'lal', 'Lalb_Chr03g0027771' => 'lal', 'Lalb_Chr06g0170041' => 'lal', 'Lalb_Chr13g0293051' => 'lal', 'Lalb_Chr15g0083671' => 'lal', 'Lalb_Chr18g0051941' => 'lal', 'Lalb_Chr19g0136861' => 'lal', 'Lalb_Chr21g0313071' => 'lal', 'Lalb_Chr24g0395001' => 'lal', 'Lj1A1151T86' => 'lonja', 'Lj1C214T4' => 'lonja', 'Lj2A24T66' => 'lonja', 'Lj2A341T40' => 'lonja', 'Lj3A935G38' => 'lonja', 'Lj3g0008635' => 'lja', 'Lj3g0027003' => 'lja', 'Lj4g0005018' => 'lja', 'Lj5g0003206' => 'lja', 'Lj6g0024369' => 'lja', 'Lsat_1_v5_gn_1_65160' => 'lsa', 'Lsat_1_v5_gn_2_103280' => 'lsa', 'Lsat_1_v5_gn_2_59740' => 'lsa', 'Lsat_1_v5_gn_6_41860' => 'lsa', 'Lsat_1_v5_gn_8_107201' => 'lsa', 'Lsat_1_v5_gn_8_17741' => 'lsa', 'Manes.03G072400' => 'mes', 'Manes.07G093800' => 'mes', 'Manes.11G153300' => 'mes', 'Manes.16G058900' => 'mes', 'Mapoly0027s0151' => 'mpo', 'MBI02_g17881_MAGBIO' => 'mbi', 'MBI18_g15814_MAGBIO' => 'mbi', 'MBI18_g17942_MAGBIO' => 'mbi', 'MBI18_g30008_MAGBIO' => 'mbi', 'MD02G1237400' => 'mdo', 'MD03G1127700' => 'mdo', 'MD05G1243100' => 'mdo', 'MD07G1074600' => 'mdo', 'MD10G1225200' => 'mdo', 'MD10G1272700' => 'mdo', 'MD11G1149900' => 'mdo', 'Medtr1g090803' => 'mtr', 'Medtr2g030405' => 'mtr', 'Medtr2g084475' => 'mtr', 'Medtr2g437720' => 'mtr', 'Medtr4g056600' => 'mtr', 'Medtr4g094795' => 'mtr', 'MELO3C006998.2' => 'cme', 'MELO3C012383.2' => 'cme', 'MELO3C026960.2' => 'cme', 'Migut.D02302' => 'egut', 'Migut.F01674' => 'egut', 'Migut.F01907' => 'egut', 'Migut.M02031' => 'egut', 'Migut.M02032' => 'egut', 'Migut.N02537' => 'egut', 'MSTRG.12347' => 'ama', 'MSTRG.18708' => 'ama', 'MSTRG.27505' => 'ama', 'MSTRG.401' => 'ama', 'MSTRG.7611' => 'ama', 'MSTRG.9127' => 'ama', 'Nitab4.5_0000107g0210' => 'nta', 'Nitab4.5_0000173g0250' => 'nta', 'Nitab4.5_0000255g0020' => 'nta', 'Nitab4.5_0000593g0360' => 'nta', 'Nitab4.5_0000614g0040' => 'nta', 'Nitab4.5_0001299g0060' => 'nta', 'Nitab4.5_0001815g0030' => 'nta', 'Nitab4.5_0004786g0060' => 'nta', 'Nitab4.5_0006341g0010' => 'nta', 'Nn2g13882' => 'nnu', 'Nn3g21570' => 'nnu', 'Nn4g24429' => 'nnu', 'Nn4g26669' => 'nnu', 'Nn6g35186' => 'nnu', 'Nn7g38417' => 'nnu', 'Oeu005281.1' => 'oeu', 'Oeu005283.1' => 'oeu', 'Oeu005285.1' => 'oeu', 'Oeu007304.1' => 'oeu', 'Oeu008365.2' => 'oeu', 'Oeu052924.1' => 'oeu', 'Oeu056660.1' => 'oeu', 'Os02g0823300' => 'osa', 'Os07g0499800' => 'osa', 'Os09g0570500' => 'osa', 'Peaxi162Scf00036g00414' => 'pax', 'Peaxi162Scf00150g10111' => 'pax', 'Peaxi162Scf00203g00142' => 'pax', 'Peaxi162Scf00253g00219' => 'pax', 'Peaxi162Scf00543g00214' => 'pax', 'Peaxi162Scf00723g00041' => 'pax', 'PGR042G0834' => 'pgr', 'PGR044G1566' => 'pgr', 'PGR119G0029' => 'pgr', 'PGSC0003DMG400000421' => 'stu', 'PGSC0003DMG400007157' => 'stu', 'PGSC0003DMG400011288' => 'stu', 'PGSC0003DMG400016919' => 'stu', 'PGSC0003DMG400027362' => 'stu', 'PGSC0003DMG401013630' => 'stu', 'Phvul.005G129700' => 'pvu', 'Phvul.007G145500' => 'pvu', 'Phvul.009G244700' => 'pvu', 'Phvul.011G087100' => 'pvu', 'Potri.001G074800' => 'ptr', 'Potri.001G215166' => 'ptr', 'Potri.003G156400' => 'ptr', 'Potri.004G217700' => 'ptr', 'Potri.008G030100' => 'ptr', 'Potri.009G003500' => 'ptr', 'Potri.010G231100' => 'ptr', 'Pp3c22_3520' => 'ppa', 'PRCOL_00005189' => 'pco', 'Prupe.2G094700' => 'ppe', 'Prupe.4G120300' => 'ppe', 'Prupe.6G114200' => 'ppe', 'Psat1g151440' => 'psa', 'Psat5g253280' => 'psa', 'Psat6g173560' => 'psa', 'Psat7g087000' => 'psa', 'Psat7g191800' => 'psa', 'PSO063G4402' => 'pso', 'PSO339G1246' => 'pso', 'PSO339G4037' => 'pso', 'PSO541G6062' => 'pso', 'PSO675G5192' => 'pso', 'PSO801G0238' => 'pso', 'QL01p014789' => 'qlo', 'QL08p053050' => 'qlo', 'QL11p010904' => 'qlo', 'RcHm_v2.0_Chr1g0336281' => 'rch', 'RcHm_v2.0_Chr5g0021761' => 'rch', 'RcHm_v2.0_Chr5g0056421' => 'rch', 'Rhsim03G0111600' => 'rsi', 'Rhsim09G0145200' => 'rsi', 'Rhsim13G0101900' => 'rsi', 'Rhsim13G0135800' => 'rsi', 'Sabra01G0052900' => 'sbr', 'Sabra03G0113400' => 'sbr', 'Sabra04G0148300' => 'sbr', 'Sabra08G0020200' => 'sbr', 'Sabra10G0179200' => 'sbr', 'SalBow3G4362' => 'sbo', 'SalBow4G1952' => 'sbo', 'SalBow6G2739' => 'sbo', 'SalBow6G4066' => 'sbo', 'SalBow8G5620' => 'sbo', 'Sc06g0008960' => 'sci', 'Sc17g0004310' => 'sci', 'Sc20g0001490' => 'sci', 'Sed0000060' => 'sed', 'Sed0016921' => 'sed', 'Sed0018505' => 'sed', 'Sed0018777' => 'sed', 'Sed0028003' => 'sed', 'SEGI_02263' => 'sgi', 'SEGI_09686' => 'sgi', 'SEGI_12818' => 'sgi', 'SEGI_14139' => 'sgi', 'SEGI_17599' => 'sgi', 'SEGI_21734' => 'sgi', 'SEGI_25695' => 'sgi', 'SEGI_29427' => 'sgi', 'SGA_v2.0_scaffold176G39390' => 'sas', 'SGA_v2.0_scaffold277G46707' => 'sas', 'SGA_v2.0_scaffold41G15750' => 'sas', 'SGA_v2.0_scaffold423G51455' => 'sas', 'SGA_v2.0_scaffold83G26460' => 'sas', 'SMO358G0436' => 'smo', 'Solyc02g082100.4' => 'sly', 'Solyc03g071680.2' => 'sly', 'Solyc06g074760.2' => 'sly', 'Solyc10g005220.3' => 'sly', 'Solyc11g007910.2' => 'sly', 'Solyc11g066500.2' => 'sly', 'Sopen02g026760' => 'spe', 'Sopen03g019920' => 'spe', 'Sopen06g031200' => 'spe', 'Sopen10g001210' => 'spe', 'Sopen11g003770' => 'spe', 'Sopen11g009750' => 'spe', 'Sopen11g026250' => 'spe', 'Sp1g26760' => 'spa', 'Sp2g09500' => 'spa', 'Sp3g08780' => 'spa', 'Sp4g10770' => 'spa', 'Sp4g17220' => 'spa', 'Sp6g38290' => 'spa', 'Sp7g18590' => 'spa', 'TAR365G0008' => 'tar', 'TAR369G0606' => 'tar', 'TAR453G0001' => 'tar', 'TAR623G0804' => 'tar', 'TAR624G0505' => 'tar', 'TAR626G1817' => 'tar', 'TAR629G3448' => 'tar', 'TAR633G0853' => 'tar', 'TAR633G2218' => 'tar', 'THA.LOC104800568' => 'tha', 'THA.LOC104811913' => 'tha', 'THA.LOC104814327' => 'tha', 'THA.LOC104816446' => 'tha', 'Thecc.02G001500' => 'tca', 'Thecc.09G296700' => 'tca', 'Thecc.10G089900' => 'tca', 'Thhalv10006896m.g' => 'esa', 'Thhalv10016236m.g' => 'esa', 'Thhalv10016344m.g' => 'esa', 'Thhalv10020131m.g' => 'esa', 'Thhalv10024247m.g' => 'esa', 'TPR.G27394' => 'tpr', 'TPR.G30936' => 'tpr', 'TPR.G31693' => 'tpr', 'TPR.G32391' => 'tpr', 'TPR.G37745' => 'tpr', 'TWI15G0953' => 'twi', 'TWI38G0101' => 'twi', 'TWI38G1849' => 'twi', 'TWI63G0053' => 'twi', 'TWI63G1213' => 'twi', 'TWI75G1588' => 'twi', 'unitig_0.g2618' => 'ugi', 'unitig_26.g9466' => 'ugi', 'unitig_26.g9467' => 'ugi', 'unitig_37.g12898' => 'ugi', 'unitig_748.g8069' => 'ugi', 'vmacro03248' => 'vma', 'vmacro03569' => 'vma', 'vmacro03570' => 'vma', 'vmacro07199' => 'vma', 'vmacro10264' => 'vma', 'VMungo0251G0395' => 'vmu', 'VMungo0720G0656' => 'vmu', 'VMungo1080G0612' => 'vmu', 'VMungo1080G1425' => 'vmu', 'VMungo1127G1387' => 'vmu', 'VMungo1309G2226' => 'vmu', 'Zm00001eb000600' => 'zma', 'Zm00001eb105360' => 'zma', 'Zm00001eb190930' => 'zma', 'Zm00001eb307770' => 'zma', 'Zm00001eb321870' => 'zma' ) $gf_id = 'HOM05D001163' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001163' ) $data_identifier = 'HOM05D001163' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 15, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 24, 'bol' => (int) 10, 'bra' => (int) 9, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 6, 'car' => (int) 5, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 6, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 3, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 9, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 6, 'oeu' => (int) 7, 'osa' => (int) 3, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 7, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 8, 'sas' => (int) 5, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 7, 'spa' => (int) 7, 'tar' => (int) 9, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 6, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321870' $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